From f1bcd02b59ad713eb4ad285623829a8daf146562 Mon Sep 17 00:00:00 2001 From: lucioric Date: Fri, 17 May 2019 02:48:42 -0500 Subject: [PATCH 01/34] Add -N option to wget of genome-fetcher.py --- .../app/bin/obsolete/genome-fetcher/genome-fetcher.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py b/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py index ae2d7c4548..d4e5fa2492 100755 --- a/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py +++ b/cellbase-app/app/bin/obsolete/genome-fetcher/genome-fetcher.py @@ -101,7 +101,7 @@ logging.debug(sp_obj['assembly']) outfile = sequence_folder+"/"+sp_short.capitalize() + ".{0}".format(sp_obj['assembly'])+".fa.gz" logging.debug(outfile) - command = "wget --tries=10 " + url_seq +" -O '"+outfile+"' -o "+outfile+".log" + command = "wget -N --tries=10 " + url_seq +" -O '"+outfile+"' -o "+outfile+".log" logging.debug(command) os.system(command) cmd = "./genome_info.pl --species '{0}' -o {1}/genome_info.json".format(sp, sequence_folder) @@ -109,7 +109,7 @@ os.system(cmd) # for i in sp_obj['chromosomes']: # outfile = seq_folder+"/chrom_"+i+".fa.gz" - # command = "wget --tries=10 " + url_seq+"/*.dna.chromosome."+i+".fa.gz -O '"+outfile+"' -o "+outfile+".log" + # command = "wget -N --tries=10 " + url_seq+"/*.dna.chromosome."+i+".fa.gz -O '"+outfile+"' -o "+outfile+".log" # logging.debug(command) # os.system(command) @@ -121,7 +121,7 @@ url_gtf = sp_obj['sequence_url'].replace("fasta", "gtf")+"{0}".format(sp_short) logging.debug(url_gtf) outfile = gene_folder+"/"+sp_short+".gtf.gz" - command = "wget --tries=10 " + url_gtf+"/*.gtf.gz -O '"+outfile+"' -o "+outfile+".log" + command = "wget -N --tries=10 " + url_gtf+"/*.gtf.gz -O '"+outfile+"' -o "+outfile+".log" logging.debug(command) os.system(command) if sp_obj['phylo'] is not 'Bacteria': @@ -159,7 +159,7 @@ variation_url = sp_obj['variation_url'] for file in variation_files: outfile = variation_folder+"/"+file - command = "wget --tries=10 " + variation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log" + command = "wget -N --tries=10 " + variation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log" logging.debug(command) os.system(command) @@ -172,7 +172,7 @@ regulation_url = sp_obj['regulation_url']+sp_short for file in regulation_files: outfile = regulation_folder+"/"+file - command = "wget --tries=10 " + regulation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log" + command = "wget -N --tries=10 " + regulation_url+"/"+file+" -O '"+outfile+"' -o "+outfile+".log" logging.debug(command) os.system(command) From b43a194316dbdce202eaf9467e8d0ee787b53636 Mon Sep 17 00:00:00 2001 From: lucioric Date: Fri, 17 May 2019 02:53:01 -0500 Subject: [PATCH 02/34] Add the -N option to wget in the Java code Add the -N option to wget in DownloadCommandExecutor.java --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 8ae3219b58..3d486cf8c7 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1165,7 +1165,7 @@ private void downloadFile(String url, String outputFileName) throws IOException, private void downloadFile(String url, String outputFileName, List wgetAdditionalArgs) throws IOException, InterruptedException { - List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", + List wgetArgs = new ArrayList<>(Arrays.asList("-N", "--tries=10", url, "-O", outputFileName, "-o", outputFileName + ".log")); if (wgetAdditionalArgs != null && !wgetAdditionalArgs.isEmpty()) { wgetArgs.addAll(wgetAdditionalArgs); From 47f4cbef7f0b2f3ac86f65bd3804a4af17089f5f Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Fri, 17 May 2019 22:57:41 +0200 Subject: [PATCH 03/34] Added existance in destination testing for files being downloaded --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 3d486cf8c7..5b5151641c 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1165,6 +1165,10 @@ private void downloadFile(String url, String outputFileName) throws IOException, private void downloadFile(String url, String outputFileName, List wgetAdditionalArgs) throws IOException, InterruptedException { + File file = new File(outputFileName); + if (file.exists()){ + logger.info("File "+outputFileName + " exists and will not be downloaded again"); + } List wgetArgs = new ArrayList<>(Arrays.asList("-N", "--tries=10", url, "-O", outputFileName, "-o", outputFileName + ".log")); if (wgetAdditionalArgs != null && !wgetAdditionalArgs.isEmpty()) { From d3ee25e488127cf6f30c37f7aba4fa5e64b3dbd8 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 00:20:47 +0200 Subject: [PATCH 04/34] Fix style, and add MongoDB installer --- .../app/cli/DownloadCommandExecutor.java | 7 +- .../clinical/variant/DOCMIndexer.java | 2 +- .../src/main/resources/configuration.json | 1232 +++++++++-------- .../test/resources/configuration.test.json | 4 +- 4 files changed, 625 insertions(+), 620 deletions(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 5b5151641c..17ea82ad56 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1166,10 +1166,11 @@ private void downloadFile(String url, String outputFileName, List wgetAd throws IOException, InterruptedException { File file = new File(outputFileName); - if (file.exists()){ - logger.info("File "+outputFileName + " exists and will not be downloaded again"); + if (file.exists()) { + logger.info("File " + outputFileName + " exists and will not be downloaded again"); + return; } - List wgetArgs = new ArrayList<>(Arrays.asList("-N", "--tries=10", url, "-O", outputFileName, "-o", + List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", outputFileName + ".log")); if (wgetAdditionalArgs != null && !wgetAdditionalArgs.isEmpty()) { wgetArgs.addAll(wgetAdditionalArgs); diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java index ec2bbe6ce5..f958d29b4b 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java @@ -30,7 +30,7 @@ public class DOCMIndexer extends ClinicalIndexer { private static final String DISEASE = "disease"; private static final String SOURCE_PUBMED_ID = "source_pubmed_id"; private static final String PMID = "PMID:"; - private static final String URL_PREFIX = "http://docm.genome.wustl.edu/variants/"; + private static final String URL_PREFIX = "http://docm.info/variants/"; private static final String HGVS = "hgvs"; private static final String GENE = "gene"; private static final String TRANSCRIPT = "transcript"; diff --git a/cellbase-core/src/main/resources/configuration.json b/cellbase-core/src/main/resources/configuration.json index 8a475f4fbe..f2f61d0b1a 100644 --- a/cellbase-core/src/main/resources/configuration.json +++ b/cellbase-core/src/main/resources/configuration.json @@ -1,616 +1,620 @@ { - "version": "v4", - "apiVersion": "${cellbase.version}", - "wiki": "https://github.com/opencb/cellbase/wiki", - "maintenanceFlagFile": "/tmp/maintenance", - "maintainerContact": "javier.lopez@genomicsengland.co.uk", - "databases": { - "mongodb": { - "host": "${CELLBASE.DB.MONGODB.HOST}", - "user": "${CELLBASE.DB.USER}", - "password": "${CELLBASE.DB.PASSWORD}", - "options": { - "authenticationDatabase": "${CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE}", - "readPreference": "${CELLBASE.DB.MONGODB.READPREFERENCE}", - "replicaSet": "${CELLBASE.DB.MONGODB.REPLICASET}", - "connectionsPerHost": 20 - } - }, - "neo4j": { - "hsapiens": { - "host": "${CELLBASE.DB.NEO4J.HOST}", - "user": "${CELLBASE.DB.USER}", - "password": "${CELLBASE.DB.PASSWORD}" - }, - "mmusculus": { - "host": "${CELLBASE.DB.NEO4J.HOST}", - "user": "${CELLBASE.DB.USER}", - "password": "${CELLBASE.DB.PASSWORD}" - } - } - }, - "defaultOutdir": "/tmp", - "download": { - "ensembl": { - "database": { - "host": "ensembldb.ensembl.org:3306", - "user": "anonymous", - "password": "" - }, - "libs": "${CELLBASE.ENSEMBL.LIBS}", - "url": { - "host": "ftp://ftp.ensembl.org/pub" - } - }, - "ensemblGenomes":{ - "database":{ - "host": "mysql-eg-publicsql.ebi.ac.uk:4157", - "user": "anonymous", - "password": "" - }, - "libs": "${CELLBASE.ENSEMBL.LIBS}", - "url":{ - "host":"ftp://ftp.ensemblgenomes.org/pub" - } - }, - "geneUniprotXref": { - "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/" - }, - "geneExpressionAtlas": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/gxa/allgenes_updown_in_organism_part_2.0.14.tab.gz" - }, - "mirbase": { - "host": "ftp://mirbase.org/pub/mirbase/CURRENT/" - }, - "mirbaseReadme": { - "host": "ftp://mirbase.org/pub/mirbase/CURRENT/README" - }, - "targetScan": { - "host": "http://hgdownload.cse.ucsc.edu/goldenPath/" - }, - "miRTarBase": { - "host": "http://mirtarbase.mbc.nctu.edu.tw/cache/download/4.5/" - }, - "uniprot": { - "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" - }, - "uniprotRelNotes": { - "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/relnotes.txt" - }, - "intact": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt" - }, - "interpro": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/protein2ipr.dat.gz" - }, - "interproRelNotes": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/release_notes.txt" - }, - "conservation": { - "host": "ftp://hgdownload.cse.ucsc.edu/goldenPath/" - }, - "gerp": { - "host": "http://mendel.stanford.edu/SidowLab/downloads/gerp/hg19.GERP_scores.tar.gz" - }, - "clinvar": { - "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2018-10.xml.gz" - }, - "clinvarSummary": { - "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz" - }, - "clinvarVariationAllele": { - "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz" - }, - "clinvarEfoTerms": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/eva/ClinVar/2015/ClinVar_Traits_EFO_Names_260615.csv" - }, - "iarctp53": { - "host": "http://p53.iarc.fr/ajax/Zipper.ashx" - }, - "docm": { - "host": "http://docm.genome.wustl.edu/api/" - }, - "docmVersion": { - "host": "http://docm.genome.wustl.edu" - }, - "dgv": { - "host": "http://dgv.tcag.ca/v106/docs" - }, - "simpleRepeats": { - "host": "http://hgdownload.cse.ucsc.edu/goldenPath" - }, - "windowMasker": { - "host": "http://hgdownload.cse.ucsc.edu/goldenPath" - }, - "genomicSuperDups": { - "host": "http://hgdownload.cse.ucsc.edu/goldenPath" - }, - "gwasCatalog": { - "host": "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2016/09/28/gwas-catalog-associations.tsv" - }, - "hpo": { - "host": "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt" - }, - "disgenet": { - "host": "http://www.disgenet.org/ds/DisGeNET/results/all_gene_disease_associations.tsv.gz" - }, - "disgenetReadme": { - "host": "http://www.disgenet.org/ds/DisGeNET/results/readme.txt" - }, - "dgidb": { - "host": "http://dgidb.org/data/interactions.tsv" - }, - "cadd": { - "host": "http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz" - }, - "reactome": { - "host": "http://www.reactome.org/download/current/biopax.zip" - } - }, - "species": { - "vertebrates": [ - { - "id": "hsapiens", - "scientificName": "Homo sapiens", - "assemblies": [ - { - "ensemblVersion":"82_37", - "name":"GRCh37" - }, - { - "ensemblVersion":"89_38", - "name":"GRCh38" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "gene_disease_association", - "variation", - "variation_functional_score", - "regulation", - "protein", - "conservation", - "clinical_variants", - "clinical", - "svs", - "repeats" - ] - }, - { - "id":"mmusculus", - "scientificName":"Mus musculus", - "assemblies":[ - { - "ensemblVersion":"82_38", - "name":"GRCm38" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "regulation", - "protein", - "conservation" - ] - }, - { - "id":"drerio", - "scientificName":"Danio rerio", - "assemblies":[ - { - "ensemblVersion":"82_10", - "name":"GRCz10" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"rnorvegicus", - "scientificName":"Rattus norvegicus", - "assemblies":[ - { - "ensemblVersion":"82_6", - "name":"Rnor_6.0" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"ptroglodytes", - "scientificName":"Pan troglodytes", - "assemblies":[ - { - "ensemblVersion":"82_214", - "name":"CHIMP2.1.4" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - }, - { - "id":"ggorilla", - "scientificName":"Gorilla gorilla", - "assemblies":[ - { - "ensemblVersion":"82_31", - "name":"gorGor3.1" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - }, - { - "id":"csabaeus", - "scientificName":"Chlorocebus sabaeus", - "assemblies":[ - { - "ensemblVersion":"82_1", - "name":"ChlSab1.1" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - }, - { - "id":"sscrofa", - "scientificName":"Sus scrofa", - "assemblies":[ - { - "ensemblVersion":"82_102", - "name":"Sscrofa10.2" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"cfamiliaris", - "scientificName":"Canis familiaris", - "assemblies":[ - { - "ensemblVersion":"82_31", - "name":"CanFam3.1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - } - ], - "metazoa":[ - { - "id":"celegans", - "scientificName":"Caenorhabditis elegans", - "assemblies":[ - { - "ensemblVersion":"29_82_245", - "name":"WBcel235" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"dmelanogaster", - "scientificName":"Drosophila melanogaster", - "assemblies":[ - { - "ensemblVersion":"29_82_6", - "name":"BDGP6" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"agambiae", - "scientificName":"Anopheles gambiae", - "assemblies":[ - { - "ensemblVersion":"29_82_4", - "name":"AgamP4" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - } - ], - "fungi":[ - { - "id":"scerevisiae", - "scientificName":"Saccharomyces cerevisiae", - "assemblies":[ - { - "ensemblVersion":"29_82_4", - "name":"R64-1-1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"afumigatus", - "scientificName":"Aspergillus fumigatus", - "assemblies":[ - { - "ensemblVersion":"29_82_2", - "name":"CADRE" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - }, - { - "id":"anidulans", - "scientificName":"Aspergillus nidulans", - "assemblies":[ - { - "ensemblVersion":"29_82_6", - "name":"ASM1142v1" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - } - ], - "protist":[ - { - "id":"pfalciparum", - "scientificName":"Plasmodium falciparum", - "assemblies":[ - { - "ensemblVersion":"29_82_3", - "name":"ASM276v1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"lmajor", - "scientificName":"Leishmania major", - "assemblies":[ - { - "ensemblVersion":"29_82_2", - "name":"ASM272v2" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - } - ], - "plants":[ - { - "id":"athaliana", - "scientificName":"Arabidopsis thaliana", - "assemblies":[ - { - "ensemblVersion":"29_82_10", - "name":"TAIR10" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation", - "protein" - ] - }, - { - "id":"osativa", - "scientificName":"Oryza sativa", - "assemblies":[ - { - "ensemblVersion":"29_82_7", - "name":"IRGSP-1.0" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - }, - { - "id":"gmax", - "scientificName":"Glycine max", - "assemblies":[ - { - "ensemblVersion":"29_82_1", - "name":"V1.0" - } - ], - "data":[ - "genome", - "genome_info", - "gene" - ] - }, - { - "id":"vvinifera", - "scientificName":"Vitis vinifera", - "assemblies":[ - { - "ensemblVersion":"29_82_3", - "name":"IGGP_12x" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - }, - { - "id":"zmays", - "scientificName":"Zea mays", - "assemblies":[ - { - "ensemblVersion":"29_82_6", - "name":"AGPv3" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - }, - { - "id":"sbicolor", - "scientificName":"Sorghum bicolor", - "assemblies":[ - { - "ensemblVersion":"29_82_14", - "name":"Sorbi1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - }, - { - "id":"slycopersicum", - "scientificName":"Solanum lycopersicum", - "assemblies":[ - { - "ensemblVersion":"29_82_250", - "name":"GCA_000188115.2" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "variation" - ] - } - ], - "virus" : [ - { - "id":"evirus", - "scientificName":"Ebola virus", - "assemblies":[ - { - "name":"KM034562v1" - } - ], - "data":[ - "genome", - "gene" - ] - } - ], - "bacteria": [ - { - "id": "mpneumoniae", - "scientificName": "Mycoplasma pneumoniae M129", - "assemblies": [ - { - "ensemblVersion":"29_82_1", - "ensemblCollection":"bacteria_0_collection", - "name":"ASM2734v1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "protein" - ] - }, - { - "id": "ecoli", - "scientificName": "Escherichia coli", - "assemblies": [ - { - "ensemblVersion":"29_82_1", - "ensemblCollection":"bacteria_91_collection", - "name":"HUSEC2011CHR1" - } - ], - "data":[ - "genome", - "genome_info", - "gene", - "protein" - ] - } - ] - } + "version": "v4", + "apiVersion": "v3", + "wiki": "https://github.com/opencb/cellbase/wiki", + "maintenanceFlagFile": "/tmp/maintenance", + "maintainerContact": "javier.lopez@genomicsengland.co.uk", + "databases": { + "mongodb": { + "host": "localhost:27017", + "user": "", + "password": "", + "options": { + "authenticationDatabase": "admin", + "readPreference": "nearest", + "replicaSet": "", + "connectionsPerHost": 20 + } + }, + "neo4j": { + "hsapiens": { + "host": "localhost:27017", + "user": "", + "password": "" + }, + "mmusculus": { + "host": "localhost:27017", + "user": "", + "password": "" + } + } + }, + "defaultOutdir": "/tmp", + "download": { + "ensembl": { + "database": { + "host": "ensembldb.ensembl.org:3306", + "user": "anonymous", + "password": "" + }, + "libs": "/srv/qgen/ensembl/ensembl-io", + "url": { + "host": "ftp://ftp.ensembl.org/pub" + } + }, + "ensemblGenomes":{ + "database":{ + "host": "mysql-eg-publicsql.ebi.ac.uk:4157", + "user": "anonymous", + "password": "" + }, + "libs": "/srv/qgen/ensembl/ensembl-io", + "url":{ + "host":"ftp://ftp.ensemblgenomes.org/pub" + } + }, + "geneUniprotXref": { + "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/" + }, + "geneExpressionAtlas": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/gxa/allgenes_updown_in_organism_part_2.0.14.tab.gz" + }, + "mirbase": { + "host": "ftp://mirbase.org/pub/mirbase/CURRENT/" + }, + "mirbaseReadme": { + "host": "ftp://mirbase.org/pub/mirbase/CURRENT/README" + }, + "targetScan": { + "host": "http://hgdownload.cse.ucsc.edu/goldenPath/" + }, + "miRTarBase": { + "host": "http://mirtarbase.mbc.nctu.edu.tw/cache/download/4.5/" + }, + "uniprot": { + "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" + }, + "uniprotRelNotes": { + "host": "ftp://ftp.uniprot.org/pub/databases/uniprot/relnotes.txt" + }, + "intact": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psimitab/intact.txt" + }, + "interpro": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/protein2ipr.dat.gz" + }, + "interproRelNotes": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/release_notes.txt" + }, + "conservation": { + "host": "ftp://hgdownload.cse.ucsc.edu/goldenPath/" + }, + "gerp": { + "host": "http://mendel.stanford.edu/SidowLab/downloads/gerp/hg19.GERP_scores.tar.gz" + }, + "clinvar": { + "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2018-10.xml.gz" + }, + "clinvarSummary": { + "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz" + }, + "clinvarVariationAllele": { + "host": "ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz" + }, + "clinvarEfoTerms": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/eva/ClinVar/2015/ClinVar_Traits_EFO_Names_260615.csv" + }, + "iarctp53": { + "host": "http://p53.iarc.fr/ajax/Zipper.ashx" + }, + "docm": { + "host": "http://docm.info/api/" + }, + "docmVersion": { + "host": "http://docm.info" + }, + "dgv": { + "host": "http://dgv.tcag.ca/v106/docs" + }, + "simpleRepeats": { + "host": "http://hgdownload.cse.ucsc.edu/goldenPath" + }, + "windowMasker": { + "host": "http://hgdownload.cse.ucsc.edu/goldenPath" + }, + "genomicSuperDups": { + "host": "http://hgdownload.cse.ucsc.edu/goldenPath" + }, + "gwasCatalog": { + "host": "ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2016/09/28/gwas-catalog-associations.tsv" + }, + "hpo": { + "host": "http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt" + }, + "disgenet": { + "host": "http://www.disgenet.org/static/disgenet_ap1/files/downloads/all_gene_disease_associations.tsv.gz" + }, + "disgenetReadme": { + "host": "http://www.disgenet.org/static/disgenet_ap1/files/downloads/readme.txt" + }, + "dgidb": { + "host": "http://dgidb.org/data/interactions.tsv" + }, + "cadd": { + "host": "http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz" + }, + "reactome": { + "host": "http://www.reactome.org/download/current/biopax.zip" + } + }, + "species": { + "vertebrates": [ + { + "id": "hsapiens", + "scientificName": "Homo sapiens", + "assemblies": [ + { + "ensemblVersion":"82_37", + "name":"GRCh37" + }, + { + "ensemblVersion":"89_38", + "name":"GRCh38_89" + }, + { + "ensemblVersion":"89", + "name":"GRCh38" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "gene_disease_association", + "variation", + "variation_functional_score", + "regulation", + "protein", + "conservation", + "clinical_variants", + "clinical", + "svs", + "repeats" + ] + }, + { + "id":"mmusculus", + "scientificName":"Mus musculus", + "assemblies":[ + { + "ensemblVersion":"82_38", + "name":"GRCm38" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "regulation", + "protein", + "conservation" + ] + }, + { + "id":"drerio", + "scientificName":"Danio rerio", + "assemblies":[ + { + "ensemblVersion":"82_10", + "name":"GRCz10" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"rnorvegicus", + "scientificName":"Rattus norvegicus", + "assemblies":[ + { + "ensemblVersion":"82_6", + "name":"Rnor_6.0" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"ptroglodytes", + "scientificName":"Pan troglodytes", + "assemblies":[ + { + "ensemblVersion":"82_214", + "name":"CHIMP2.1.4" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + }, + { + "id":"ggorilla", + "scientificName":"Gorilla gorilla", + "assemblies":[ + { + "ensemblVersion":"82_31", + "name":"gorGor3.1" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + }, + { + "id":"csabaeus", + "scientificName":"Chlorocebus sabaeus", + "assemblies":[ + { + "ensemblVersion":"82_1", + "name":"ChlSab1.1" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + }, + { + "id":"sscrofa", + "scientificName":"Sus scrofa", + "assemblies":[ + { + "ensemblVersion":"82_102", + "name":"Sscrofa10.2" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"cfamiliaris", + "scientificName":"Canis familiaris", + "assemblies":[ + { + "ensemblVersion":"82_31", + "name":"CanFam3.1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + } + ], + "metazoa":[ + { + "id":"celegans", + "scientificName":"Caenorhabditis elegans", + "assemblies":[ + { + "ensemblVersion":"29_82_245", + "name":"WBcel235" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"dmelanogaster", + "scientificName":"Drosophila melanogaster", + "assemblies":[ + { + "ensemblVersion":"29_82_6", + "name":"BDGP6" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"agambiae", + "scientificName":"Anopheles gambiae", + "assemblies":[ + { + "ensemblVersion":"29_82_4", + "name":"AgamP4" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + } + ], + "fungi":[ + { + "id":"scerevisiae", + "scientificName":"Saccharomyces cerevisiae", + "assemblies":[ + { + "ensemblVersion":"29_82_4", + "name":"R64-1-1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"afumigatus", + "scientificName":"Aspergillus fumigatus", + "assemblies":[ + { + "ensemblVersion":"29_82_2", + "name":"CADRE" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + }, + { + "id":"anidulans", + "scientificName":"Aspergillus nidulans", + "assemblies":[ + { + "ensemblVersion":"29_82_6", + "name":"ASM1142v1" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + } + ], + "protist":[ + { + "id":"pfalciparum", + "scientificName":"Plasmodium falciparum", + "assemblies":[ + { + "ensemblVersion":"29_82_3", + "name":"ASM276v1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"lmajor", + "scientificName":"Leishmania major", + "assemblies":[ + { + "ensemblVersion":"29_82_2", + "name":"ASM272v2" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + } + ], + "plants":[ + { + "id":"athaliana", + "scientificName":"Arabidopsis thaliana", + "assemblies":[ + { + "ensemblVersion":"29_82_10", + "name":"TAIR10" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation", + "protein" + ] + }, + { + "id":"osativa", + "scientificName":"Oryza sativa", + "assemblies":[ + { + "ensemblVersion":"29_82_7", + "name":"IRGSP-1.0" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + }, + { + "id":"gmax", + "scientificName":"Glycine max", + "assemblies":[ + { + "ensemblVersion":"29_82_1", + "name":"V1.0" + } + ], + "data":[ + "genome", + "genome_info", + "gene" + ] + }, + { + "id":"vvinifera", + "scientificName":"Vitis vinifera", + "assemblies":[ + { + "ensemblVersion":"29_82_3", + "name":"IGGP_12x" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + }, + { + "id":"zmays", + "scientificName":"Zea mays", + "assemblies":[ + { + "ensemblVersion":"29_82_6", + "name":"AGPv3" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + }, + { + "id":"sbicolor", + "scientificName":"Sorghum bicolor", + "assemblies":[ + { + "ensemblVersion":"29_82_14", + "name":"Sorbi1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + }, + { + "id":"slycopersicum", + "scientificName":"Solanum lycopersicum", + "assemblies":[ + { + "ensemblVersion":"29_82_250", + "name":"GCA_000188115.2" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "variation" + ] + } + ], + "virus" : [ + { + "id":"evirus", + "scientificName":"Ebola virus", + "assemblies":[ + { + "name":"KM034562v1" + } + ], + "data":[ + "genome", + "gene" + ] + } + ], + "bacteria": [ + { + "id": "mpneumoniae", + "scientificName": "Mycoplasma pneumoniae M129", + "assemblies": [ + { + "ensemblVersion":"29_82_1", + "ensemblCollection":"bacteria_0_collection", + "name":"ASM2734v1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "protein" + ] + }, + { + "id": "ecoli", + "scientificName": "Escherichia coli", + "assemblies": [ + { + "ensemblVersion":"29_82_1", + "ensemblCollection":"bacteria_91_collection", + "name":"HUSEC2011CHR1" + } + ], + "data":[ + "genome", + "genome_info", + "gene", + "protein" + ] + } + ] + } } diff --git a/cellbase-lib/src/test/resources/configuration.test.json b/cellbase-lib/src/test/resources/configuration.test.json index 95264e5eb5..3deb3417cc 100644 --- a/cellbase-lib/src/test/resources/configuration.test.json +++ b/cellbase-lib/src/test/resources/configuration.test.json @@ -108,10 +108,10 @@ "host": "http://p53.iarc.fr/ajax/Zipper.ashx" }, "docm": { - "host": "http://docm.genome.wustl.edu/api/" + "host": "http://docm.info/api/" }, "docmVersion": { - "host": "http://docm.genome.wustl.edu" + "host": "http://docm.info" }, "dgv": { "host": "http://dgv.tcag.ca/v106/docs" From 09300395cc7a770dce283ecd81582eb6458ef71c Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 03:32:30 +0200 Subject: [PATCH 05/34] Added file size comparizon in redownload intelligent avouder --- .../cellbase/app/cli/DownloadCommandExecutor.java | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 17ea82ad56..b557ea1661 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1167,8 +1167,17 @@ private void downloadFile(String url, String outputFileName, List wgetAd File file = new File(outputFileName); if (file.exists()) { - logger.info("File " + outputFileName + " exists and will not be downloaded again"); - return; + FTPClient ftpClient = new FTPClient(); + // code to connect and login.... + + FTPFile remotefile = ftpClient.mlistFile(outputFileName); + long remotesize = remotefile.getSize(); + long localsize = file.length(); + logger.info("File " + outputFileName + " exists, with size " +localsize + "vs " + remotesize + " in remote and will not be downloaded again"); + if ( remotesize == localsize ) { + logger.info("Download avoided because the files has the same size"); + return; + } } List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", outputFileName + ".log")); From e07e140aa8f28552b0d8672f7c4bc8c5beccbac5 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 03:50:24 +0200 Subject: [PATCH 06/34] Fixed some typos --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index b557ea1661..429342b9c0 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1174,7 +1174,7 @@ private void downloadFile(String url, String outputFileName, List wgetAd long remotesize = remotefile.getSize(); long localsize = file.length(); logger.info("File " + outputFileName + " exists, with size " +localsize + "vs " + remotesize + " in remote and will not be downloaded again"); - if ( remotesize == localsize ) { + if (remotesize == localsize) { logger.info("Download avoided because the files has the same size"); return; } From 4a18aa707d7c77820f59307015ffd7a2dcd3b660 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 03:54:01 +0200 Subject: [PATCH 07/34] Fixed other typos --- .../app/cli/DownloadCommandExecutor.java | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 429342b9c0..3a835148db 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1167,16 +1167,17 @@ private void downloadFile(String url, String outputFileName, List wgetAd File file = new File(outputFileName); if (file.exists()) { - FTPClient ftpClient = new FTPClient(); - // code to connect and login.... - - FTPFile remotefile = ftpClient.mlistFile(outputFileName); - long remotesize = remotefile.getSize(); - long localsize = file.length(); - logger.info("File " + outputFileName + " exists, with size " +localsize + "vs " + remotesize + " in remote and will not be downloaded again"); + FTPClient ftpClient = new FTPClient(); + // code to connect and login.... + + FTPFile remotefile = ftpClient.mlistFile(outputFileName); + long remotesize = remotefile.getSize(); + long localsize = file.length(); + logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + + remotesize + " in remote and will not be downloaded again"); if (remotesize == localsize) { - logger.info("Download avoided because the files has the same size"); - return; + logger.info("Download avoided because the files has the same size"); + return; } } List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", From 76def550495bd9caab4131227e9981c7fb08d9e1 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 04:01:57 +0200 Subject: [PATCH 08/34] Fix typos (3) --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 3a835148db..1dfe8a81c0 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1173,8 +1173,8 @@ private void downloadFile(String url, String outputFileName, List wgetAd FTPFile remotefile = ftpClient.mlistFile(outputFileName); long remotesize = remotefile.getSize(); long localsize = file.length(); - logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + - remotesize + " in remote and will not be downloaded again"); + logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + + remotesize + " in remote and will not be downloaded again"); if (remotesize == localsize) { logger.info("Download avoided because the files has the same size"); return; From 56afa9da13a936d94d9eb687a41fb8077a072872 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 04:35:08 +0200 Subject: [PATCH 09/34] Fix style typo (4) --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index 1dfe8a81c0..a8e575b378 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1173,7 +1173,8 @@ private void downloadFile(String url, String outputFileName, List wgetAd FTPFile remotefile = ftpClient.mlistFile(outputFileName); long remotesize = remotefile.getSize(); long localsize = file.length(); - logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + long locallastmodified = file.lastModified(); + logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + remotesize + " in remote and will not be downloaded again"); if (remotesize == localsize) { logger.info("Download avoided because the files has the same size"); From 061674274746dea11d6e89eb5b09158200a136fa Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 05:33:42 +0200 Subject: [PATCH 10/34] Add references previously missed to import --- .../opencb/cellbase/app/cli/DownloadCommandExecutor.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index a8e575b378..c4919d97ab 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -24,6 +24,8 @@ import org.apache.commons.collections.map.HashedMap; import org.apache.commons.io.FilenameUtils; import org.apache.commons.io.IOUtils; +import org.apache.commons.net.ftp.FTPClient; +import org.apache.commons.net.ftp.FTPFile; import org.apache.commons.lang.StringUtils; import org.opencb.cellbase.core.config.Species; import org.opencb.commons.utils.FileUtils; @@ -1177,9 +1179,12 @@ private void downloadFile(String url, String outputFileName, List wgetAd logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + remotesize + " in remote and will not be downloaded again"); if (remotesize == localsize) { - logger.info("Download avoided because the files has the same size"); + logger.info("Download avoided because the files have the same size"); return; } + //If the filestamps differ, regardless of the timestamps downloads the file + Calendar remotets = FTPFile.getTimeStamp(); + logger.info("local ts " + locallastmodified + "wheras remote ts is " + remotets.toString()); } List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", outputFileName + ".log")); From 5b9982e84f79996b10c3c725088470a4ea38a13a Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 05:55:00 +0200 Subject: [PATCH 11/34] Mudyfy pom.xml co include apache commons net --- pom.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pom.xml b/pom.xml index f112c3ebd6..ee681a9bbd 100644 --- a/pom.xml +++ b/pom.xml @@ -123,6 +123,11 @@ commons-datastore-core ${java-common-libs.version} + + org.opencb.commons.net + commons-datastore-net + ${java-common-libs.version} + From f9530366bdd2b4fbdfeb1df7c15d4604eeb33abb Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 06:11:34 +0200 Subject: [PATCH 12/34] Moify pom.xml --- pom.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index ee681a9bbd..b1839d086b 100644 --- a/pom.xml +++ b/pom.xml @@ -25,6 +25,7 @@ 4.6.2 1.8 3.7.0 + 3.7.0 1.4.3 0.1.0 2.8.4 @@ -124,9 +125,9 @@ ${java-common-libs.version} - org.opencb.commons.net - commons-datastore-net - ${java-common-libs.version} + commons-net + commons-net + ${commons-net.version} From b4ebf854549b3f9b28611ea18cf790624fbdee9b Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 07:49:12 +0200 Subject: [PATCH 13/34] Cmt --- cellbase-app/pom.xml | 7 ++++++- cellbase-server/pom.xml | 1 + pom.xml | 7 +------ 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml index 9f19c7d984..4dba74ff7f 100644 --- a/cellbase-app/pom.xml +++ b/cellbase-app/pom.xml @@ -45,7 +45,12 @@ commons-io commons-io - 2.4 + 3.6 + + + commons-net + commons-net + ${commons-net.version} org.spockframework diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml index eb142d4630..ba771f663a 100644 --- a/cellbase-server/pom.xml +++ b/cellbase-server/pom.xml @@ -85,6 +85,7 @@ org.apache.maven.plugins maven-install-plugin + 3.2.2 install diff --git a/pom.xml b/pom.xml index b1839d086b..4300a75686 100644 --- a/pom.xml +++ b/pom.xml @@ -25,7 +25,7 @@ 4.6.2 1.8 3.7.0 - 3.7.0 + 3.6 1.4.3 0.1.0 2.8.4 @@ -124,11 +124,6 @@ commons-datastore-core ${java-common-libs.version} - - commons-net - commons-net - ${commons-net.version} - From 7ea7a64f7f114915f8e82b853f15b54abea52789 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 08:09:12 +0200 Subject: [PATCH 14/34] Cmt --- cellbase-server/pom.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml index ba771f663a..eb142d4630 100644 --- a/cellbase-server/pom.xml +++ b/cellbase-server/pom.xml @@ -85,7 +85,6 @@ org.apache.maven.plugins maven-install-plugin - 3.2.2 install From 67b0fecc3eb96482c8e627755f2db8529bd7888d Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 08:15:58 +0200 Subject: [PATCH 15/34] Cmt --- cellbase-app/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml index 4dba74ff7f..f5d9e466d9 100644 --- a/cellbase-app/pom.xml +++ b/cellbase-app/pom.xml @@ -45,7 +45,7 @@ commons-io commons-io - 3.6 + 2.4 commons-net From 8cc94e02676e37970133bfbc8868d4b3b2bf9431 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sat, 18 May 2019 09:03:17 +0200 Subject: [PATCH 16/34] Java code stable --- .../org/opencb/cellbase/app/cli/DownloadCommandExecutor.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java index c4919d97ab..5ec342e51c 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java @@ -1176,14 +1176,14 @@ private void downloadFile(String url, String outputFileName, List wgetAd long remotesize = remotefile.getSize(); long localsize = file.length(); long locallastmodified = file.lastModified(); - logger.info("File " + outputFileName + " exists, with size " + localsize + "vs " + logger.info("File " + outputFileName + " exists, with size " + localsize + " vs " + remotesize + " in remote and will not be downloaded again"); if (remotesize == localsize) { logger.info("Download avoided because the files have the same size"); return; } //If the filestamps differ, regardless of the timestamps downloads the file - Calendar remotets = FTPFile.getTimeStamp(); + Calendar remotets = remotefile.getTimestamp(); logger.info("local ts " + locallastmodified + "wheras remote ts is " + remotets.toString()); } List wgetArgs = new ArrayList<>(Arrays.asList("--tries=10", url, "-O", outputFileName, "-o", From ba6e5e8fac3e375f43fa692c492b442d227c19d0 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sun, 19 Jul 2020 09:02:37 +0200 Subject: [PATCH 17/34] Cmt --- .gitignore | 0 .gitmodules | 0 LICENSE | 0 README.md | 0 cellbase-app/app/bin/obsolete/gene-chunkIds.js | 0 .../app/bin/obsolete/genome-fetcher/CHECKSUMS | 0 .../app/bin/obsolete/genome-fetcher/species.json | 0 .../bin/obsolete/genome-fetcher/species_info.json | 0 .../bin/obsolete/genome-fetcher/species_info.txt | 0 cellbase-app/app/bin/obsolete/variation-chunkIds.js | 0 cellbase-app/app/example/5000_variants.vcf.gz | Bin cellbase-app/app/example/BasicTest.Json | 0 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.../app/mongodb-scripts/variation-indexes.js | 0 .../variation_functional_score-indexes.js | 0 .../mongodb-scripts/variation_phenotype-indexes.js | 0 .../variation_phenotype_annotation-indexes.js | 0 cellbase-app/pom.xml | 0 .../java/org/opencb/cellbase/app/CellBaseMain.java | 0 .../cellbase/app/cli/BuildCommandExecutor.java | 0 .../opencb/cellbase/app/cli/CliOptionsParser.java | 0 .../opencb/cellbase/app/cli/CommandExecutor.java | 0 .../cellbase/app/cli/DownloadCommandExecutor.java | 0 .../org/opencb/cellbase/app/cli/EtlCommons.java | 0 .../cellbase/app/cli/LoadCommandExecutor.java | 0 .../cellbase/app/cli/PostLoadCommandExecutor.java | 0 .../cellbase/app/cli/QueryCommandExecutor.java | 0 .../cellbase/app/cli/QueryGrpcCommandExecutor.java | 0 .../app/cli/VariantAnnotationCommandExecutor.java | 0 .../cli/variant/annotation/BenchmarkDataWriter.java | 0 .../app/cli/variant/annotation/BenchmarkTask.java | 0 .../annotation/CellBaseLocalVariantAnnotator.java | 0 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...sites.annot.subset.atomic.left.split.test.vcf.gz | Bin .../proband.duprem.atomic.left.split.vcf.gz | Bin ...sites.annot.subset.atomic.left.split.test.vcf.gz | Bin ...sites.annot.subset.atomic.left.split.test.vcf.gz | Bin .../resources/variationParser/genotype_code.txt.gz | Bin .../resources/variationParser/seq_region.txt.gz | Bin .../test/resources/variationParser/source.txt.gz | Bin .../variationParser/transcript_variation.txt.gz | Bin .../test/resources/variationParser/variation.txt.gz | Bin .../variationParser/variation_feature.txt.gz | Bin .../variationParser/variation_synonym.txt.gz | Bin .../src/test/resources/vep-example-output.txt | 0 cellbase-client/pom.xml | 0 .../cellbase/client/config/ClientConfiguration.java | 0 .../opencb/cellbase/client/config/GrpcConfig.java | 0 .../opencb/cellbase/client/config/RestConfig.java | 0 .../cellbase/client/grpc/CellbaseGrpcClient.java | 0 .../opencb/cellbase/client/grpc/GeneGrpcClient.java | 0 .../client/grpc/GenomicRegionGrpcClient.java 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a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/GenomicRegionClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/GenomicRegionClientTest.java old mode 100644 new mode 100755 diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/MetaClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/MetaClientTest.java old mode 100644 new mode 100755 diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/ProteinClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/ProteinClientTest.java old mode 100644 new mode 100755 diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/TranscriptClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/TranscriptClientTest.java old mode 100644 new mode 100755 diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java 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a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/Species.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/Species.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/ClinicalVariant.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/ClinicalVariant.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/ClinvarPublicSet.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/ClinvarPublicSet.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/Cosmic.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/Cosmic.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/clinical/gwas/Gwas.java 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a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/genedisease/Disgenet.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/genedisease/Disgenet.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/BiopaxPathway.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/BiopaxPathway.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/ComplexComponent.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/ComplexComponent.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/Interaction.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/Interaction.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/PhysicalEntity.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/PhysicalEntity.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/SubPathway.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/pathway/SubPathway.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/FunctionPrediction.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/FunctionPrediction.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Interaction.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Interaction.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Interactor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Interactor.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Psimi.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Psimi.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Score.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/Score.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/XRef.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/protein/XRef.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/ConservedRegion.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/ConservedRegion.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaDisease.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaDisease.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaGene.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaGene.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaGeneToMature.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaGeneToMature.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaMature.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaMature.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaTarget.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/regulatory/MirnaTarget.java old mode 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b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/ConsequenceType.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/GenomicVariantEffect.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/GenomicVariantEffect.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Mutation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Mutation.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/MutationPhenotypeAnnotation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/MutationPhenotypeAnnotation.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Phenotype.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Phenotype.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/PopulationFrequency.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/PopulationFrequency.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/SampleGenotype.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/SampleGenotype.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/StructuralVariation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/StructuralVariation.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/TranscriptVariation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/TranscriptVariation.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Variation.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Variation.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Xref.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/common/variation/Xref.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/CellBaseConfiguration.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/CellBaseConfiguration.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DatabaseCredentials.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DatabaseCredentials.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Databases.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Databases.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/DownloadProperties.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Species.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/Species.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/config/SpeciesProperties.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/config/SpeciesProperties.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseLoader.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/loader/CellBaseLoader.java old mode 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b/cellbase-core/src/main/java/org/opencb/cellbase/core/monitor/Monitor.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseFileSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseFileSerializer.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseJsonFileSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseJsonFileSerializer.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseSerializer.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/serializer/CellBaseSerializer.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/AnnotationBasedPhasedQueryManager.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/ClinicalPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/ClinicalPhasedQueryManager.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/CustomAnnotationPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/CustomAnnotationPhasedQueryManager.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PhasedQueryManager.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PopulationFrequencyPhasedQueryManager.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/PopulationFrequencyPhasedQueryManager.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/CellBaseNormalizerSequenceAdaptor.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/CellBaseNormalizerSequenceAdaptor.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeBNDCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeBNDCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCNVGainCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCNVGainCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeDeletionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeDeletionCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeGenericRegionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeGenericRegionCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeInsertionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeInsertionCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeMNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeMNVCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeSNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/ConsequenceTypeSNVCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/UnsupportedURLVariantFormat.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/UnsupportedURLVariantFormat.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/CdnaCoord.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/CdnaCoord.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsDeletionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsDeletionCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsInsertionCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsInsertionCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsSNVCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsSNVCalculator.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsStringBuilder.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsStringBuilder.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/gene_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/gene_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/generic_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/generic_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/genomic_region_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/genomic_region_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/regulatory_region_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/regulatory_region_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/transcript_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/transcript_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/variant_annotation_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/variant_annotation_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/proto/protobuf/opencb/service/variant_service.proto b/cellbase-core/src/main/proto/protobuf/opencb/service/variant_service.proto old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/resources/configuration.json b/cellbase-core/src/main/resources/configuration.json old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/resources/log4j.properties b/cellbase-core/src/main/resources/log4j.properties old mode 100644 new mode 100755 diff --git a/cellbase-core/src/main/resources/org/opencb/cellbase/core/variation/variation_consequences.properties b/cellbase-core/src/main/resources/org/opencb/cellbase/core/variation/variation_consequences.properties old mode 100644 new mode 100755 diff --git a/cellbase-core/src/test/java/org/opencb/cellbase/core/CellBaseConfigurationTest.java b/cellbase-core/src/test/java/org/opencb/cellbase/core/CellBaseConfigurationTest.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/test/java/org/opencb/cellbase/core/variant/VariantAnnotatorRunnerTest.java b/cellbase-core/src/test/java/org/opencb/cellbase/core/variant/VariantAnnotatorRunnerTest.java old mode 100644 new mode 100755 diff --git a/cellbase-core/src/test/resources/cellBaseProperties_test.json b/cellbase-core/src/test/resources/cellBaseProperties_test.json old mode 100644 new mode 100755 diff --git a/cellbase-core/src/test/resources/gene.json b/cellbase-core/src/test/resources/gene.json old mode 100644 new mode 100755 diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml old mode 100644 new mode 100755 diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/MongoDBCollectionConfiguration.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/MongoDBCollectionConfiguration.java old mode 100644 new mode 100755 diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/VariantMongoIterator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/VariantMongoIterator.java old mode 100644 new mode 100755 diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalLegacyMongoDBAdaptor.java old mode 100644 new mode 100755 diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptor.java 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100644 new mode 100755 diff --git a/clients/python/Dockerfile b/clients/python/Dockerfile old mode 100644 new mode 100755 diff --git a/clients/python/HISTORY.rst b/clients/python/HISTORY.rst old mode 100644 new mode 100755 diff --git a/clients/python/LICENSE.txt b/clients/python/LICENSE.txt old mode 100644 new mode 100755 diff --git a/clients/python/pycellbase/commons.py b/clients/python/pycellbase/commons.py old mode 100644 new mode 100755 diff --git a/clients/python/requirements.txt b/clients/python/requirements.txt old mode 100644 new mode 100755 diff --git a/clients/python/setup.cfg b/clients/python/setup.cfg old mode 100644 new mode 100755 diff --git a/clients/python/tests/test_cbcclient.py b/clients/python/tests/test_cbcclient.py old mode 100644 new mode 100755 diff --git a/clients/python/tests/test_cbconfig.py b/clients/python/tests/test_cbconfig.py old mode 100644 new mode 100755 diff --git a/clients/python/tests/test_commons.py b/clients/python/tests/test_commons.py old mode 100644 new mode 100755 diff --git a/clients/python/tests/testresources/config.json b/clients/python/tests/testresources/config.json old mode 100644 new mode 100755 diff --git a/clients/python/tests/testresources/config.yml b/clients/python/tests/testresources/config.yml old mode 100644 new mode 100755 diff --git a/clients/python/tools/cbtools.py b/clients/python/tools/cbtools.py old mode 100644 new mode 100755 diff --git a/clients/python/use_case.ipynb b/clients/python/use_case.ipynb old mode 100644 new mode 100755 diff --git a/pom.xml b/pom.xml old mode 100644 new mode 100755 diff --git a/regulatory_region.test.json b/regulatory_region.test.json old mode 100644 new mode 100755 From 0b5f9bec306557fc77744acb358a903276d15d30 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Tue, 15 Sep 2020 10:37:44 +0200 Subject: [PATCH 18/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index bb4156e230..333668a646 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit bb4156e2301ba4e0b3fb49aba9d945faf4fa604a +Subproject commit 333668a64645a8e1833058b5d5b006f7b963238f From 136a7a4358aaeb644d3eaccbecd0e771d42b0288 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Mon, 19 Oct 2020 07:25:18 +0200 Subject: [PATCH 19/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 333668a646..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 333668a64645a8e1833058b5d5b006f7b963238f +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From 85d02c8b109f07158f4911d7676d9f2f405ea0dd Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Wed, 21 Oct 2020 04:07:18 +0200 Subject: [PATCH 20/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..bb4156e230 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit bb4156e2301ba4e0b3fb49aba9d945faf4fa604a From f874ccaa74128fb6ce7a78d573ef3346d855f521 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Wed, 21 Oct 2020 04:24:12 +0200 Subject: [PATCH 21/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index bb4156e230..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit bb4156e2301ba4e0b3fb49aba9d945faf4fa604a +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From 1f8f4a321c8081d8ab5cac2f89ec77f6f78d5186 Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Wed, 21 Oct 2020 10:00:53 +0200 Subject: [PATCH 22/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 333668a646..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 333668a64645a8e1833058b5d5b006f7b963238f +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 653dc7898fff55797eab88994dc0750329d3587b Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Wed, 21 Oct 2020 10:02:43 +0200 Subject: [PATCH 23/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 52938f02608379ee35d4f72c466a16f04fb9be59 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Wed, 21 Oct 2020 10:45:20 +0200 Subject: [PATCH 24/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 333668a646..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 333668a64645a8e1833058b5d5b006f7b963238f +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From ae5b0915ed8e35547fcdbb9a7657cd118659899d Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Wed, 21 Oct 2020 10:47:08 +0200 Subject: [PATCH 25/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 82893362b0..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From ba5061559c43815c97b254f29b7df25bcb0f6758 Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Wed, 21 Oct 2020 23:05:03 +0200 Subject: [PATCH 26/34] ommit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 35c7f83118991773e0acba304e4005d34635f88d Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Wed, 21 Oct 2020 23:13:11 +0200 Subject: [PATCH 27/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 82893362b0..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From d4a20655fdd4c38a3dd286aca6f1b32939410f75 Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Wed, 21 Oct 2020 23:21:11 +0200 Subject: [PATCH 28/34] Commit --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index e67f8541f8..60a042e5f9 100755 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,3 @@ [submodule "cellbase-web/lib/jsorolla"] path = cellbase-web/lib/jsorolla - url = https://github.com/opencb/jsorolla.git + url = https://github.com/Lucioric2000/jsorolla.git From 8348d64cc3bffb811c0b8582371619686c82a0ea Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Sat, 1 May 2021 23:17:51 -0500 Subject: [PATCH 29/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 560b2baf1b49f6de27a0bdf6f4da00456ca7ed77 Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Sat, 1 May 2021 23:19:56 -0500 Subject: [PATCH 30/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index bb4156e230..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit bb4156e2301ba4e0b3fb49aba9d945faf4fa604a +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From 0d9f80b69a4c1b7c1c4734f5560c0891c3018ce2 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Sun, 2 May 2021 07:58:34 +0200 Subject: [PATCH 31/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 1a3a13e4de2499f798341106a004bc3bf05c09cd Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Sun, 2 May 2021 03:29:02 -0500 Subject: [PATCH 32/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 82893362b0..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 From f5c7e2896ae8fd977e35126efa2b98c16fab8e3c Mon Sep 17 00:00:00 2001 From: Lucio Ricardo Montero Valenzuela Date: Sun, 2 May 2021 03:49:06 -0500 Subject: [PATCH 33/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index c9ba7f9ece..82893362b0 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0 +Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 From 23b468b5036adc1c56afbe5f60e2581d675ac5e1 Mon Sep 17 00:00:00 2001 From: Lucio Montero Date: Fri, 7 May 2021 23:34:12 +0200 Subject: [PATCH 34/34] Commit --- cellbase-web/lib/jsorolla | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellbase-web/lib/jsorolla b/cellbase-web/lib/jsorolla index 82893362b0..c9ba7f9ece 160000 --- a/cellbase-web/lib/jsorolla +++ b/cellbase-web/lib/jsorolla @@ -1 +1 @@ -Subproject commit 82893362b03c3933bc536b4f976c4e4a92bd5a61 +Subproject commit c9ba7f9eced52be0048a270b7fb885ed91314ff0